Staphylococcal Phages Adapt to New Hosts by Extensive Attachment Site Variability

A growing number of humans are being infected by antibiotic resistant Staphylococcus aureus originating from livestock. The preference of S. aureus for humans or animals is in part determined by factors encoded by viruses (phages) that reside in the bacterial genome.

Capturing site-to-site variability through Hierarchical Bayesian calibration of a process-based dynamic vegetation model

Process-based ecosystem models help us understand and predict ecosystem processes, but using them has long involved a difficult choice between performing data- and labor-intensive site-level calibrations or relying on general parameters that may not reflect local conditions. Hierarchical Bayesian (HB) calibration provides a third option that frees modelers from assuming model parameters to be completely generic or completely site-specific and allows a formal distinction between prediction at known calibration sites and “out-of-sample” prediction to new sites. Here, we compare calibrations of a process-based dynamic vegetation model to eddy-covariance data across 12 temperate deciduous Ameriflux sites fit using either site-specific, joint cross-site, or HB approaches. To be able to apply HB to computationally demanding process-based models we introduce a novel emulator-based HB calibration tool, which we make available through the PEcAn community cyberinfrastructure. Using these calibrations to make predictions at held-out tower sites, we show that the joint cross-site calibration is falsely over-confident because it neglects parameter variability across sites and therefore underestimates variance in parameter distributions. By showing which parameters show high site-to-site variability, HB calibration also formally gives us a structure that can detect which process representations are missing from the models and prioritize errors based on the magnitude of the associated uncertainty. For example, in our case-study, we were able to identify large site-to-site variability in the parameters related to the temperature responses of respiration and photosynthesis, associated with a lack of thermal acclimation and adaptation in the model. Moving forward, HB approaches present important new opportunities for statistical modeling of the spatiotemporal variability in modeled parameters and processes that yields both new insights and improved predictions.

Multi-centre, multi-vendor 7 Tesla fMRI reproducibility of hand digit representation in the human somatosensory cortex

Whilst considerable progress has been made in using ultra-high field fMRI to study brain function at fine spatial resolution, methods are generally optimized at a single site and do not translate to studies where multiple sites are required for sufficient subject recruitment. With a recent increase in installations of human 7 T systems, there is now the opportunity to establish a framework for multi-site 7 T fMRI studies. However, an understanding of the inter-site variability of fMRI measurements is required for datasets to be combined across sites. To address this, we employ a hand digit localization task and compare across-site and within-site reproducibility of 7 T fMRI to a hand digit localization task which requires fine spatial resolution to resolve individual digit representations. As part of the UK7T Network “Travelling Heads” study, 10 participants repeated the same hand digit localization task at five sites with whole-body 7T MRI systems to provide a measure of inter-site variability. A subset of the participants (2 per site) performed repeated sessions at each site for measurement of intra-site reproducibility. Dice’s overlap coefficient was used to assess reproducibility, with hand region inter-site Dice = 0.70±0.04 significantly lower than intrasite Dice = 0.76±0.06, with similar trends for the individual digit maps. Although slightly lower than intra-site reproducibility, the inter-site reproducibility results are consistent with previous single site reproducibility measurements, providing evidence that multi-site 7 T fMRI studies are feasible. These results can be used to inform sample size calculations for future multi-site somatomotor mapping studies.

Guideline-Directed Medical Therapy in Patients with Chronic Kidney Disease Undergoing Peripheral Vascular Intervention

<b><i>Introduction:</i></b> Guideline-directed medical therapy (GDMT) is imperative to improve cardiovascular and limb outcomes for patients with critical limb ischemia (CLI), especially amongst those at highest risk for poor outcomes, including those with comorbid chronic kidney disease (CKD). Our objective was to examine GDMT prescription rates and their variation across individual sites for patients with CLI undergoing peripheral vascular interventions (PVIs), by their comorbid CKD status. <b><i>Methods:</i></b> Patients with CLI who underwent PVI (October 2016–April 2019) were included from the Vascular Quality Initiative (VQI) database. CKD was defined as GFR &#x3c;60 mL/min/1.73 m². GDMT included the composite use of antiplatelet therapy and a statin, as well as an angiotensin-converting enzyme inhibitor or angiotensin receptor blocker if hypertension was present. The use of GDMT before and after the index procedure was summarized in those with and without CKD. Adjusted median odds ratios (MORs) for site variability were calculated. <b><i>Results:</i></b> The study included 28,652 patients, with a mean age of 69.4 ± 11.7 years, and 40.8% were females. A total of 47.5% had CKD. Patients with CKD versus those without CKD had lower prescription rates both before (31.7% vs. 38.9%) and after (36.5% vs. 48.8%) PVI (<i>p</i> &#x3c; 0.0001). Significant site variability was observed in the delivery of GDMT in both the non-CKD and CKD groups before and after PVI (adjusted MORs: 1.31–1.41). <b><i>Discussion/Conclusion:</i></b> In patients with CLI undergoing PVI, patients with comorbid CKD were less likely to receive GDMT. Significant variability of GDMT was observed across sites. These findings indicate that significant improvements must be made in the medical management of patients with CLI, particularly in patients at high risk for poor clinical outcomes.

Large Multisite Clinical Field Study Characterizing Contamination Levels in Patient Used Endoscopes After Manual Cleaning

Background: Multiple outbreaks multidrug-resistant organisms (MDROs) have been associated with flexible endoscopes resulting in unacceptable patient mortality and morbidity. Evidence highlights the importance of effective cleaning to achieve effective high-level disinfection (HLD). This study presents an analysis of >700,000 measurements of adenosine-triphosphate (ATP) contamination levels found in flexible endoscopes after manual cleaning. Method: This 2018–2019 study consists of 702,768 measurements of ATP levels found in the suction/biopsy channel of instruments used on patients after manual cleaning: gastroscopes (267,533 measurements from 223 sites), duodenoscopes (123,697 measurements from 161 sites), colonoscopes (252,249 measurements from 229 sites), and bronchoscopes (59,289 measurements from 107 sites). Sites were located across the United States and employed protocols that included routine cleaning verification performed by the reprocessing technicians using a handheld luminometer and the associated ATP water test (3M Clean-Trace). Results: Figure 1 shows a boxplot analysis of the ATP levels by endoscope type. Upper gastrointestinal (GI) endoscopes (gastroscopes and duodenoscopes) show a significantly (P < .005) greater level of ATP contamination after manual cleaning. The pairwise mean differences are all significant (P < .005) except for colonoscopes when compared to bronchoscopes (P = .203). Also shown on Fig. 1 is a literature supported adequate cleanliness value of 200 RLUs [=2.3log(RLUs)] (MJ Alfa et al.; Am J Infec Control 2013;41:245–253 and ANSI/AAMI ST91; 2015). A 95% confidence interval analysis performed against this literature value (Table 1) showed that a high number of gastroscopes (12%) and duodenoscopes (10%) are not adequately clean. Figure 2 shows a box-plot analysis of the data set by endoscope type and by site. There is significant (P < .005) site-to-site variability for all endoscope types as demonstrated by variation in mean values, box size, and many outliers. Conclusions: This study highlights the importance of using a quantitative cleaning verification method to better understand process capability and to provide more robust quality assurance for manual cleaning. Significant differences were detected in the level of cleanliness between upper GI scopes and lower GI scopes and bronchoscopes. When compared to a literature-supported level for adequate cleanliness, upper GI scopes exhibited failure rates in excess of 10%. Furthermore, significant site-to-site variability occurred, and many outliers fell well beyond the normal process envelope, representing significant cleaning lapses. Root causes to these concerning findings could range from inadequate execution of the cleaning protocol, to device design, to age and existing damage that could prevent achieving adequate cleaning and possibly impair the effectiveness of HLD.Funding: NoneDisclosures: Marco Bommarito, 3M (salary)

Generation and evaluation of synthetic cone penetration test (CPT) data using various spatial interpolation techniques

The cone penetration test (CPT) has been widely used in many geotechnical engineering applications, including soil identification and classification, and evaluation of different soil properties. However, the uncertainties associated with site variation are typical characteristics of subsurface soil conditions that cannot be ignored. Therefore, the effect of site variability on the correlated soil properties from collected field data, such as CPT data, obtained from discrete locations across the site needs to be evaluated. In this study, six well-established spatial interpolation techniques — ordinary kriging (OK), simple kriging (SK), universal kriging (UK), inverse distance weight (IDW), spline, and natural neighbor (NaN) — were investigated to evaluate the best interpolation method for incorporating site variability. Six CPT test sites were used to evaluate the performance of these spatial interpretation methods. For each site, CPT profiles at specified locations were generated using the different interpolation techniques, and the generated CPT profiles were compared with the measured CPT profiles. The best-fit line of measured versus predicted cone tip resistance (qc) values, mean bias factor (λ), coefficient of variation (COV), and root mean square error (RMSE) were calculated for each CPT profile and used as a criteria for evaluating the different spatial interpolation methods. The results of this study demonstrated the ability of these spatial interpolation methods for generating CPT profiles with good accuracy. The slope of best-fit line of measured versus predicted qc ranges from 0.93 to 0.95, the mean of λ ranges from 0.90 to 0.98, and the COV ranges from 0.34 to 0.53. The IDW, OK, and SK showed the best spatial interpolation methods (in order) for four out of the six CPT sites. For site 4, OK, IDW, and SK showed the best spatial interpolation methods (in order); while for site 5, the three best spatial interpolation techniques are SK, IDW, and OK (in order).